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@gregcaporaso
gregcaporaso / notes.md
Last active Mar 28, 2019
vsearch-based sequence dereplication through generation of a biom table
View notes.md

This depends on biom version >= 2.1.5, < 2.2.0 and vsearch >= 1.7.0.

Please note that all of this is highly experimental. I'm keeping these notes as I work with this approach. For published work, I still recommend using standard pipelines, such as those in QIIME 1.9.1.

$ biom --version
biom, version 2.1.5

$ vsearch --version
vsearch v1.7.0_osx_x86_64, 16.0GB RAM, 8 cores
@gregcaporaso
gregcaporaso / neighbor-joining-experiments.ipynb
Created Jun 11, 2014
initial experiments with implementing neighbor joining for scikit-bio
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@gregcaporaso
gregcaporaso / qiime2-issue190.ipynb
Created Dec 1, 2016
QIIME 2 issue #190 example
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View jgcaporaso-qiime2-scipy2016.ipynb
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@gregcaporaso
gregcaporaso / qiime-exercise.ipynb
Created Apr 5, 2016
Final assignment for BIO/CS 499/599 (Spring 2016)
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View artifact-demo.ipynb
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gregcaporaso / check_illumina_barcodes.py
Created Dec 3, 2013
Script for performing some basic testing on Illumina amplicon sequencing primers as described in: http://www.nature.com/ismej/journal/v6/n8/full/ismej20128a.html
View check_illumina_barcodes.py
#!/usr/bin/env python
# File created on 01 Dec 2011
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.3.0-dev"
__maintainer__ = "Greg Caporaso"
View fq_qual.py
#!/usr/bin/env python
from sys import argv
from random import random
from cogent.parse.fastq import MinimalFastqParser
from cogent.draw.distribution_plots import generate_box_plots
from qiime.quality import ascii_to_phred33
from qiime.util import qiime_open
def fastq_quality_plots(fastq_records,
@gregcaporaso
gregcaporaso / compare_pre_post_distances.py
Last active Dec 27, 2015
Code for comparing groups (e.g., treatment and control) of pre/post UniFrac distances to determine if one group's microbiomes are more stable than the other.
View compare_pre_post_distances.py
#!/usr/bin/env python
# Authors: Greg Caporaso, John Chase
# Questions: Contact gregcaporaso@gmail.com
# Step 1: Generate lists of pre/post sample ids on a per-individual basis
# qiime.group.extract_per_individual_states_from_sample_metadata
# will let you generate a dict of individual id to (pre sample-id, post sample-id)
# Step 2: Extract distances for pre/post sample ids
# qiime.parse.parse_distmat_to_dict
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